Agent-based management systems for many-core platforms : rigorous design and efficient implementation

Due to various advantages such as flexibility, scalability and updatability, software intensive systems are increasingly embedded in everyday life. The constantly growing number of functions executed by these systems requires a high level of performance from the underlying platform. The main approach to incrementing performance has been the increase of operating frequency of a chip. However, this has led to the problem of power dissipation, which has shifted the focus of research to parallel and distributed computing. Parallel many-core platforms can provide the required level of computational power along with low power consumption. On the one hand, this enables parallel execution of highly intensive applications. With their computational power, these platforms are likely to be used in various application domains: from home use electronics (e.g., video processing) to complex critical control systems. On the other hand, the utilization of the resources has to be efficient in terms of performance and power consumption. However, the high level of on-chip integration results in the increase of the probability of various faults and creation of hotspots leading to thermal problems. Additionally, radiation, which is frequent in space but becomes an issue also at the ground level, can cause transient faults. This can eventually induce a faulty execution of applications. Therefore, it is crucial to develop methods that enable efficient as well as resilient execution of applications. The main objective of the thesis is to propose an approach to design agentbased systems for many-core platforms in a rigorous manner. When designing such a system, we explore and integrate various dynamic reconfiguration mechanisms into agents functionality. The use of these mechanisms enhances resilience of the underlying platform whilst maintaining performance at an acceptable level. The design of the system proceeds according to a formal refinement approach which allows us to ensure correct behaviour of the system with respect to postulated properties. To enable analysis of the proposed system in terms of area overhead as well as performance, we explore an approach, where the developed rigorous models are transformed into a high-level implementation language. Specifically, we investigate methods for deriving fault-free implementations from these models into, e.g., a hardware description language, namely VHDL.

Rapid test for the evaluation of the activity of the prodrug hydroxymethylnitrofurazone in the processing of Trypanosoma cruzi messenger RNAs

No fully effective treatment has been developed since the discovery of Chagas' disease by Carlos Chagas in 1909. Since drug-resistant Trypanosoma cruzi strains are occurring and the current therapy is effectiveness in the acute phase but with various adverse side effects, more studies are needed to characterize the susceptibility of T. cruzi to new drugs. Many natural and/or synthetic substances showing trypanocidal activity have been used, even though they are not likely to be turned into clinically approved drugs. Originally, drug screening was performed using natural products, with only limited knowledge of the molecular mechanism involved in the development of diseases. Trans-splicing, which is unusual RNA processing reaction and occurs in nematodes and trypanosomes, implies the processing of polycistronic transcription units into individual mRNAs; a short transcript spliced leader (SL RNA) is trans-spliced to the acceptor pre-mRNA, giving origin to the mature mRNA. In the present study, permeable cells of T. cruzi epimastigote forms (Y, BOL and NCS strains) were treated to evaluate the interference of two drugs (hydroxymethylnitrofurazone - NFOH-121 and nitrofurazone) in the trans-splicing reaction using silver-stained PAGE analysis. Both drugs induced a significant reduction in RNA processing at concentrations from 5 to 12.5 µM. These data agreed with the biological findings, since the number of parasites decreased, especially with NFOH-121. This proposed methodology allows a rapid and cost-effective screening strategy for detecting drug interference in the trans-splicing mechanism of T. cruzi.

Magnetization studies of polystyrene/multiwall carbon nanotube composite films

Lappeenranta University of Technology School of Technology Technical Physics Evgenii Zhukov MAGNETIZATION STUDIES OF POLYSTYRENE/MULTIWALL CARBON NANOTUBE COMPOSITE FILMS Master’s thesis 2015 55 pages, 41 pictures, 9 Tables. Examiners: Professor Erkki Lähderanta D.Sc. Ivan Zakharchuk Keywords: polystyrene, multi-walled carbon nanotubes, MWCNT, composite, magnetization, SQUID. In this thesis magnetic properties of polystyrene/multiwall carbon nanotube (MWCNT) composites are investigated with Quantum Design SQUID magnetometer (MPMS XL). The surface of the composite films is studied via BRUKER Multimode 8 Atomic Force Microscope, as well. The polystyrene/MWCNT composites have been prepared by the group of professor Okotrub (Physics Chemistry of Nanomaterials laboratory, Nikolaev Institute of Inorganic Chemistry, Russia). The composite films have been prepared by solution processing and stretching method. The approximate length and inner diameter of the MWCNTs used in fabrication are 260 μm and 10 nm, respectively. The content of MWCNTs is 1 and 2.5 contents percent (wt%) for studied samples. The stretching of the samples is 30% for samples with 1 and 2.5 wt% content, and one sample with 1 wt% loading of MWCNTs is 100% stretched. MWCNTs aligned perpendicular to a silicon substrate are used as a reference sample. The magnetization field dependencies of the samples exhibit hysteresis behavior. The values of saturation magnetization of composite films are much less compared to that of the reference sample. The saturation magnetization coercitivity field value drops with decrease of MWCNT content. At high magnetic fields strong presence of diamagnetism is observed. Measurements in magnetic field parallel and perpendicular to the composite plate display anisotropy with respect to the direction of stretching. Temperature dependences of magnetization for all samples display difference between zero-field cooled and field-cooled curves of magnetization. This divergence confirms the presence of magnetic interactions in the material. The atomic force microscopy study of the composites’ surfaces revealed that they are relatively smooth and the nanotubes are aligned with the axis of stretching to some extent. 

How auditory temporal processing deficits relate to dyslexia

Studies have shown that dyslexic children present a deficiency in the temporal processing of auditory stimuli applied in rapid succession. However, discussion continues concerning the way this deficiency can be influenced by temporal variables of auditory processing tests. Therefore, the purpose of the present study was to analyze by auditory temporal processing tests the effect of temporal variables such as interstimulus intervals, stimulus duration and type of task on dyslexic children compared to a control group. Of the 60 children evaluated, 33 were dyslexic (mean age = 10.5 years) and 27 were normal controls (mean age = 10.8 years). Auditory processing tests assess the abilities of discrimination and ordering of stimuli in relation to their duration and frequency. Results showed a significant difference in the average accuracy of control and dyslexic groups considering each variable (interstimulus intervals: 47.9 ± 5.5 vs 37.18 ± 6.0; stimulus duration: 61.4 ± 7.6 vs 50.9 ± 9.0; type of task: 59.9 ± 7.9 vs 46.5 ± 9.0) and the dyslexic group demonstrated significantly lower performance in all situations. Moreover, there was an interactive effect between the group and the duration of stimulus variables for the frequency-pattern tests, with the dyslexic group demonstrating significantly lower results for short durations (53.4 ± 8.2 vs 48.4 ± 11.1), as opposed to no difference in performance for the control group (62.2 ± 7.1 vs 60.6 ± 7.9). These results support the hypothesis that associates dyslexia with auditory temporal processing, identifying the stimulus-duration variable as the only one that unequally influenced the performance of the two groups.

Effect of escitalopram on the processing of emotional faces

Serotonin has been implicated in the neurobiology of depressive and anxiety disorders, but little is known about its role in the modulation of basic emotional processing. The aim of this study was to determine the effect of the selective serotonin reuptake inhibitor, escitalopram, on the perception of facial emotional expressions. Twelve healthy male volunteers completed two experimental sessions each, in a randomized, balanced order, double-blind design. A single oral dose of escitalopram (10 mg) or placebo was administered 3 h before the task. Participants were presented to a task composed of six basic emotions (anger, disgust, fear, happiness, sadness, and surprise) that were morphed between neutral and each standard emotion in 10% steps. Escitalopram facilitated the recognition of sadness and inhibited the recognition of happiness in male, but not female faces. No drug effect on subjective measures was detected. These results confirm that serotonin modulates the recognition of emotional faces, and suggest that the gender of the face can have a role in this modulation. Further studies including female volunteers are needed.

Effect of auditory training on the middle latency response in children with (central) auditory processing disorder

The purpose of this study was to determine the middle latency response (MLR) characteristics (latency and amplitude) in children with (central) auditory processing disorder [(C)APD], categorized as such by their performance on the central auditory test battery, and the effects of these characteristics after auditory training. Thirty children with (C)APD, 8 to 14 years of age, were tested using the MLR-evoked potential. This group was then enrolled in an 8-week auditory training program and then retested at the completion of the program. A control group of 22 children without (C)APD, composed of relatives and acquaintances of those involved in the research, underwent the same testing at equal time intervals, but were not enrolled in the auditory training program. Before auditory training, MLR results for the (C)APD group exhibited lower C3-A1 and C3-A2 wave amplitudes in comparison to the control group [C3-A1, 0.84 µV (mean), 0.39 (SD - standard deviation) for the (C)APD group and 1.18 µV (mean), 0.65 (SD) for the control group; C3-A2, 0.69 µV (mean), 0.31 (SD) for the (C)APD group and 1.00 µV (mean), 0.46 (SD) for the control group]. After training, the MLR C3-A1 [1.59 µV (mean), 0.82 (SD)] and C3-A2 [1.24 µV (mean), 0.73 (SD)] wave amplitudes of the (C)APD group significantly increased, so that there was no longer a significant difference in MLR amplitude between (C)APD and control groups. These findings suggest progress in the use of electrophysiological measurements for the diagnosis and treatment of (C)APD.

Effects of conventional vs high-dose rocuronium on the QTc interval during anesthesia induction and intubation in patients undergoing coronary artery surgery: a randomized, double-blind, parallel trial

Myocardial ischemia, as well as the induction agents used in anesthesia, may cause corrected QT interval (QTc) prolongation. The objective of this randomized, double-blind trial was to determine the effects of high- vs conventional-dose bolus rocuronium on QTc duration and the incidence of dysrhythmias following anesthesia induction and intubation. Fifty patients about to undergo coronary artery surgery were randomly allocated to receive conventional-dose (0.6 mg/kg, group C, n=25) or high-dose (1.2 mg/kg, group H, n=25) rocuronium after induction with etomidate and fentanyl. QTc, heart rate, and mean arterial pressure were recorded before induction (T0), after induction (T1), after rocuronium (just before laryngoscopy; T2), 2 min after intubation (T3), and 5 min after intubation (T4). The occurrence of dysrhythmias was recorded. In both groups, QTc was significantly longer at T3 than at baseline [475 vs 429 ms in group C (P=0.001), and 459 vs 434 ms in group H (P=0.005)]. The incidence of dysrhythmias in group C (28%) and in group H (24%) was similar. The QTc after high-dose rocuronium was not significantly longer than after conventional-dose rocuronium in patients about to undergo coronary artery surgery who were induced with etomidate and fentanyl. In both groups, compared with baseline, QTc was most prolonged at 2 min after intubation, suggesting that QTc prolongation may be due to the nociceptive stimulus of intubation.

Metronomic chemotherapy in the neoadjuvant setting: results of two parallel feasibility trials (TraQme and TAME) in patients with HER2+ and HER2− locally advanced breast cancer

Neoadjuvant chemotherapy has practical and theoretical advantages over adjuvant chemotherapy strategy in breast cancer (BC) management. Moreover, metronomic delivery has a more favorable toxicity profile. The present study examined the feasibility of neoadjuvant metronomic chemotherapy in two cohorts [HER2+ (TraQme) and HER2− (TAME)] of locally advanced BC. Twenty patients were prospectively enrolled (TraQme, n=9; TAME, n=11). Both cohorts received weekly paclitaxel at 100 mg/m2 during 8 weeks followed by weekly doxorubicin at 24 mg/m2 for 9 weeks in combination with oral cyclophosphamide at 100 mg/day (fixed dose). The HER2+ cohort received weekly trastuzumab. The study was interrupted because of safety issues. Thirty-six percent of patients in the TAME cohort and all patients from the TraQme cohort had stage III BC. Of note, 33% from the TraQme cohort and 66% from the TAME cohort displayed hormone receptor positivity in tumor tissue. The pathological complete response rates were 55% and 18% among patients enrolled in the TraQme and TAME cohorts, respectively. Patients in the TraQme cohort had more advanced BC stages at diagnosis, higher-grade pathological classification, and more tumors lacking hormone receptor expression, compared to the TAME cohort. The toxicity profile was also different. Two patients in the TraQme cohort developed pneumonitis, and in the TAME cohort we observed more hematological toxicity and hand-foot syndrome. The neoadjuvant metronomic chemotherapy regimen evaluated in this trial was highly effective in achieving a tumor response, especially in the HER2+ cohort. Pneumonitis was a serious, unexpected adverse event observed in this group. Further larger and randomized trials are warranted to evaluate the association between metronomic chemotherapy and trastuzumab treatment.

Evaluation of total carotenoids, alpha- and beta-carotene in carrots (Daucus carota L.) during home processing

This study aims to analyze the influence of dehydration and different preparation methods during home processing related toalpha-carotene, beta-carotene and total carotenoids stability in carrots. Vitamin A values were evaluated after different treatments. Thus, carrots were submitted to steam cooking, water cooking with and without pressure, moist/dry cooking and conventional dehydration. Determination of alpha- and beta-carotenes was made by High-Performance Liquid Chromatography (HPLC) (conditions were developed by us) using spectrophotometric detection visible-UV at 470 nm; a RP-18 column and methanol: acetonitrile: ethyl acetate (80: 10: 10) as mobile phase. Total carotenoids quantification was made by 449 nm spectrophotometer. The retention of the analyzed carotenoids ranged from 60.13 to 85.64%. Water cooking without pressure promoted higher retention levels of alpha- and beta-carotene and vitamin A values, while water cooking with pressure promoted higher retention levels of total carotenoids. Dehydration promoted the highest carotenoid losses. The results showed that, among the routinely utilized methods under domestic condition, cooking without pressure, if performed under controlled time and temperature, is the best method as it reduces losses in the amount of alpha- and beta-carotene, the main carotenoids present in the carrots. Despite the significant carotenoid losses, carrots prepared through domestic methods, remain a rich source of provitamin A.

Processing of spent nickelcatalyst for fat recovery

Spent nickel catalyst (SNC) has the potential of insulting the quality of the environment in a number of ways. Its disposal has a pollution effect. Optimum recovery of fat from SNC, could save the environment and reduce the oil loss. Hexane has been the solvent of choice for oil extraction. Alternative solvents considered to have been safer have been evaluated. Hexane, isopropanol, ethanol and heptane were examined using soxhlet extraction. While hexane is more efficient in oil recovery from SNC, isopropanol proved to be very good in clear separation of oil from waste material and also provides high solvent recovery compared to other solvents. Isopropanol extraction with chill separation of miscella into lower oil-rich phase, and an upper, solvent-rich recyclable phase save mush energy of vaporization for distilling. An aqueous extraction process with immiscible solvent assisted was tested. Solvent like hexane added to SNC, and water added later with continuous stirring. The mixture was stirred for about 30 minutes, prior to centrifugation. Aqueous process extracted less amount of oil compared to solvent extraction.

Effect of processing and roasting on the antioxidant activity of coffee brews

The aim of this work was to evaluate the effect of processing and roasting on the antioxidant activity of coffee brews. Brews prepared with light, medium and dark roasted coffees were analyzed. The pH, total solids content, polyphenols content, reducing substances and chlorogenic acids content were determined. The antioxidant activity of aqueous extracts, the guaicol decolorizing and the capacity to inhibit lipid peroxidation were also analyzed. The antioxidant activity of coffee brews were concentration-dependent. A progressive antioxidant activity and polyphenols content was observed decreasing with roasting. The light roasted coffee showed the highest antioxidant activity and dark roasted coffee showed the lowest antioxidant activity. The results indicate that the ingestion of coffee brews prepared with light and medium roasted coffees might protect cells from oxidative stress damages.

Implementing Green IT approach for transferring Big Data over Parallel Data Link

The whole research of the current Master Thesis project is related to Big Data transfer over Parallel Data Link and my main objective is to assist the Saint-Petersburg National Research University ITMO research team to accomplish this project and apply Green IT methods for the data transfer system. The goal of the team is to transfer Big Data by using parallel data links with SDN Openflow approach. My task as a team member was to compare existing data transfer applications in case to verify which results the highest data transfer speed in which occasions and explain the reasons. In the context of this thesis work a comparison between 5 different utilities was done, which including Fast Data Transfer (FDT), BBCP, BBFTP, GridFTP, and FTS3. A number of scripts where developed which consist of creating random binary data to be incompressible to have fair comparison between utilities, execute the Utilities with specified parameters, create log files, results, system parameters, and plot graphs to compare the results. Transferring such an enormous variety of data can take a long time, and hence, the necessity appears to reduce the energy consumption to make them greener. In the context of Green IT approach, our team used Cloud Computing infrastructure called OpenStack. It’s more efficient to allocated specific amount of hardware resources to test different scenarios rather than using the whole resources from our testbed. Testing our implementation with OpenStack infrastructure results that the virtual channel does not consist of any traffic and we can achieve the highest possible throughput. After receiving the final results we are in place to identify which utilities produce faster data transfer in different scenarios with specific TCP parameters and we can use them in real network data links.

Electric paralyzation and reduction of weight loss in the processing of round-cooked spiny lobsters

This study proposes alternatives to the current methods of processing round-cooked lobster. The paralyzation of lobsters with direct electric shock consumes 10.526 x 10-3 kWh, which is significantly less than the 11 kWh required by the traditional thermal-shock method (based on 60 kg of lobsters). A better weight gain was obtained by immersion of paralyzed lobsters in brine before cooking. Systematic trials combining 3, 6, or 9% brine concentrations with immersion periods of 15, 30, or 45 minutes were performed in order to determine the best combinations. A mathematical model was designed to predict the weight gain of lobsters of different sizes in any combination of treatments. For small lobsters, a 45 minutes immersion in 6% brine gave the best response in terms of weight gain (4.7%) and cooking produced a weight loss of only 1.34% in relation to fresh lobster weight. For medium-sized lobsters, a 45 minutes immersion in 9% brine produced a weight gain of 2.64%, and cooking a weight gain of 1.08%. For large lobsters, a 45 minutes immersion in 6% brine produced a weight gain of 3.87%, and cooking a weight gain of 1.62%.

Identification of main contamination points by hygiene indicator microorganisms in beef processing plants

The microbiological quality of beef and meat products is strongly influenced by the conditions of hygiene prevailing during their production and handling. Without proper hygienic control, the environment in slaughterhouses and butcher shops can act as an important source of microbiological contamination. To identify the main points of microbiological contamination in the beef processing chain, 443 samples of equipment, installations and products were collected from 11 establishments (1 slaughterhouse and 10 butcher shops) located in the state of Paraná, Brazil. The microbiological quality of all the samples was evaluated using Petri dishes to obtain counts of mesophilic aerobes (AC), total coliforms, Escherichia coli (EC), yeasts and molds (YM). The main contamination points identified in butcher shops, in decreasing order, were stainless steel boxes, beef tenderizers, grinders, knives, mixers, sausage stuffers, plastic boxes, floors and drains. In the slaughterhouse, these points were sausage stuffers, platforms, floors and drains. The most severely contaminated products were fresh sausages and ground beef. This information about the main points of microbiological contamination in the beef processing chain is expected to aid professionals responsible for hygiene in similar establishments to set up proper hygienic procedures to prevent or reduce microbiological contamination of beef and meat products.